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The collection includes articles from PSI research groups and the broader community.
The Research Library is no longer being updated. Please explore the previous submissions, or find the PSI’s latest research articles in the PSI Publications Portal.
September 2008
CE-SSCP and CE-FLA, simple and high-throughput alternatives for fungal diversity studies
Zinger, L., Gury, J., Alibeu, O., Rioux, D., Gielly, L. et al.
J Microbiol Methods 72, 42-53 (2008)
Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli
Zimmerman, M. D., Proudfoot, M., Yakunin, A. and Minor, W.
J Mol Biol 378, 215-26 (2008)
Alkaloid biosynthesis: metabolism and trafficking
Ziegler, J. and Facchini, P. J.
Annu Rev Plant Biol 59, 735-69 (2008)
Understanding protein evolution: from protein physics to Darwinian selection
Zeldovich, K. B. and Shakhnovich, E. I.
Annu Rev Phys Chem 59, 105-27 (2008)
Host-bacterial coevolution and the search for new drug targets
Zaneveld, J., Turnbaugh, P. J., Lozupone, C., Ley, R. E., Hamady, M. et al.
Curr Opin Chem Biol 12, 109-14 (2008)
Spatiotemporal heterogeneity of plankton communities in Lake Donghu, China, as revealed by PCR-denaturing gradient gel electrophoresis and its relation to biotic and abiotic factors
Yu, Y., Yan, Q. and Feng, W.
FEMS Microbiol Ecol 63, 328-37 (2008)
A novel retrieval system for nearly complete microbial genomic fragments from soil samples
Yu, W. H., Su, S. C. and Lee, C. Y.
J Microbiol Methods 72, 197-205 (2008)
Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering
Yooseph, S., Li, W. and Sutton, G.
BMC Bioinformatics 9, 182 (2008)
[RIKEN structural genomics/proteomics initiative]
Yokoyama, S., Kigawa, T., Shirouzu, M., Miyano, M. and Kuramitsu, S.
Tanpakushitsu Kakusan Koso 53, 632-7 (2008)
The integration of personalized and systems medicine: bioinformatics support for pharmacogenomics and drug discovery
Yan, Q.
Methods Mol Biol 448, 1-19 (2008)
Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution
Xu, Q., Kozbial, P., McMullan, D., Krishna, S. S., Brittain, S. M. et al.
Proteins 71, 1546-52 (2008)
Isolation and characterization of alkane hydroxylases from a metagenomic library of Pacific deep-sea sediment
Xu, M., Xiao, X. and Wang, F.
Extremophiles 12, 255-62 (2008)
Discovery of virulence factors of pathogenic bacteria
Wu, H. J., Wang, A. H. and Jennings, M. P.
Curr Opin Chem Biol 12, 93-101 (2008)
Metagenomics: read length matters
Wommack, K. E., Bhavsar, J. and Ravel, J.
Appl Environ Microbiol 74, 1453-63 (2008)
Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures
Wlodawer, A., Minor, W., Dauter, Z. and Jaskolski, M.
Febs J 275, 1-21 (2008)
Metaproteomics provides functional insight into activated sludge wastewater treatment
Wilmes, P., Wexler, M. and Bond, P. L.
PLoS ONE 3, e1778 (2008)
The Sorcerer II Global Ocean Sampling Expedition: metagenomic characterization of viruses within aquatic microbial samples
Williamson, S. J., Rusch, D. B., Yooseph, S., Halpern, A. L., Heidelberg, K. B. et al.
PLoS ONE 3, e1456 (2008)
Immuno-proteomic approach to excitation--contraction coupling in skeletal and cardiac muscle: molecular insights revealed by the mitsugumins
Weisleder, N., Takeshima, H. and Ma, J.
Cell Calcium 43, 1-8 (2008)
Structural genomics and drug discovery: all in the family
Weigelt, J., McBroom-Cerajewski, L. D., Schapira, M., Zhao, Y. and Arrowmsmith, C. H.
Curr Opin Chem Biol 12, 32-9 (2008)
Genomics, environmental genomics and the issue of microbial species
Ward, D. M., Cohan, F. M., Bhaya, D., Heidelberg, J. F., Kuhl, M. et al.
Heredity 100, 207-19 (2008)
Fine-scale Population Structure of Accumulibacter phosphatis in Enhanced Biological Phosphorus Removal Sludge
Wang, Q., Shao, Y., Huong, V. T., Park, W., Park, J. M. et al.
J Microbiol Biotechnol 18, 1290-7 (2008)
Enriching plant microbiota for a metagenomic library construction
Wang, H. X., Geng, Z. L., Zeng, Y. and Shen, Y. M.
Environ Microbiol (2008)
[Structural and functional biology for post translational modification and transport in eukaryotes]
Wakatsuki, S., Kato, R., Kawasaki, M., Igarashi, N. and Masahiko, H.
Tanpakushitsu Kakusan Koso 53, 628-31 (2008)
Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico)
Valenzuela-Encinas, C., Neria-Gonzalez, I., Alcantara-Hernandez, R. J., Enriquez-Aragon, J. A., Estrada-Alvarado, I. et al.
Extremophiles 12, 247-54 (2008)
Predicting 3D structures of protein-protein complexes
Vakser, I. A. and Kundrotas, P.
Curr Pharm Biotechnol 9, 57-66 (2008)
PSI has to live and become PCI: Protein Complex Initiative
Vakser, I. A.
Structure 16, 1-3 (2008)
A common catalytic mechanism for proteins of the HutI family
Tyagi, R., Eswaramoorthy, S., Burley, S. K., Raushel, F. M. and Swaminathan, S.
Biochemistry 47, 5608-15 (2008)
Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome
Turnbaugh, P. J., Backhed, F., Fulton, L. and Gordon, J. I.
Cell Host Microbe 3, 213-23 (2008)
SAR11 marine bacteria require exogenous reduced sulphur for growth
Tripp, H. J., Kitner, J. B., Schwalbach, M. S., Dacey, J. W., Wilhelm, L. J. et al.
Nature 452, 741-4 (2008)
Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms
Tourna, M., Freitag, T. E., Nicol, G. W. and Prosser, J. I.
Environ Microbiol 10, 1357-64 (2008)
Protein structure fitting and refinement guided by cryo-EM density
Topf, M., Lasker, K., Webb, B., Wolfson, H., Chiu, W. et al.
Structure 16, 295-307 (2008)
Novel thermophilic and thermostable lipolytic enzymes from a Thailand hot spring metagenomic library
Tirawongsaroj, P., Sriprang, R., Harnpicharnchai, P., Thongaram, T., Champreda, V. et al.
J Biotechnol 133, 42-9 (2008)
Integrated analytical strategies for the study of phosphorylation and glycosylation in proteins
Temporini, C., Calleri, E., Massolini, G. and Caccialanza, G.
Mass Spectrom Rev 27, 207-36 (2008)
[Structural genomics on development and differentiation of organisms and replication and repair of DNA]
Tanokura, M., Nagata, K. and Asano, A.
Tanpakushitsu Kakusan Koso 53, 612-5 (2008)
Estimating the extent of horizontal gene transfer in metagenomic sequences
Tamames, J. and Moya, A.
BMC Genomics 9, 136 (2008)
Interactive proteomics: what lies ahead?
Suter, B., Kittanakom, S. and Stagljar, I.
Biotechniques 44, 681-91 (2008)
Portal protein diversity and phage ecology
Sullivan, M. B., Coleman, M. L., Quinlivan, V., Rosenkrantz, J. E., Defrancesco, A. S. et al.
Environ Microbiol (2008)
[From structures to functions: annotation by structural bioinformatics]
Standley, D. M. and Nakamura, H.
Tanpakushitsu Kakusan Koso 53, 638-44 (2008)
Protein structure databases with new web services for structural biology and biomedical research
Standley, D. M., Kinjo, A. R., Kinoshita, K. and Nakamura, H.
Brief Bioinform 9, 276-85 (2008)
Yeasts associated to Traditional Balsamic Vinegar: Ecological and technological features
Solieri, L. and Giudici, P.
Int J Food Microbiol 125, 36-45 (2008)
Crystal structure of the MACPF domain of human complement protein C8 alpha in complex with the C8 gamma subunit
Slade, D. J., Lovelace, L. L., Chruszcz, M., Minor, W., Lebioda, L. et al.
J Mol Biol 379, 331-42 (2008)
Computational prediction of protein-protein interactions
Skrabanek, L., Saini, H. K., Bader, G. D. and Enright, A. J.
Mol Biotechnol 38, 1-17 (2008)
Biodiversity, chemical diversity and drug discovery
Singh, S. B. and Pelaez, F.
Prog Drug Res 65, 141, 143-74 (2008)
Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation
Simmons, S. L., Dibartolo, G., Denef, V. J., Goltsman, D. S., Thelen, M. P. et al.
PLoS Biol 6, e177 (2008)
Actinorhodopsins: proteorhodopsin-like gene sequences found predominantly in non-marine environments
Sharma, A. K., Zhaxybayeva, O., Papke, R. T. and Doolittle, W. F.
Environ Microbiol 10, 1039-56 (2008)
Structural biology. Protein structure initiative: phase 3 or phase out
Service, R. F.
Science 319, 1610-3 (2008)
Structural biology. Researchers hone their homology tools
Service, R. F.
Science 319, 1612 (2008)
The JCSG MR pipeline: optimized alignments, multiple models and parallel searches
Schwarzenbacher, R., Godzik, A. and Jaroszewski, L.
Acta Crystallogr D Biol Crystallogr 64, 133-40 (2008)
A multi-angular mass spectrometric view at cyclic nucleotide dependent protein kinases: in vivo characterization and structure/function relationships
Scholten, A., Aye, T. T. and Heck, A. J.
Mass Spectrom Rev 27, 331-53 (2008)
Assembly of viral metagenomes from yellowstone hot springs
Schoenfeld, T., Patterson, M., Richardson, P. M., Wommack, K. E., Young, M. et al.
Appl Environ Microbiol 74, 4164-74 (2008)
Rapid DNA library construction for functional genomic and metagenomic screening
Schmitz, J. E., Daniel, A., Collin, M., Schuch, R. and Fischetti, V. A.
Appl Environ Microbiol 74, 1649-52 (2008)
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology
Schluter, A., Bekel, T., Diaz, N. N., Dondrup, M., Eichenlaub, R. et al.
J Biotechnol (2008)
A statistical toolbox for metagenomics: assessing functional diversity in microbial communities
Schloss, P. D. and Handelsman, J.
BMC Bioinformatics 9, 34 (2008)
Host-bacteria homeostasis in the healthy and inflamed gut
Sansonetti, P. J.
Curr Opin Gastroenterol 24, 435-9 (2008)
Photosynthetic genes in viral populations with a large genomic size range from Norwegian coastal waters
Sandaa, R. A., Clokie, M. and Mann, N. H.
FEMS Microbiol Ecol 63, 2-11 (2008)
The genetic basis for indole-diterpene chemical diversity in filamentous fungi
Saikia, S., Nicholson, M. J., Young, C., Parker, E. J. and Scott, B.
Mycol Res 112, 184-99 (2008)
The bacterial chromosome
Saier, M. H., Jr.
Crit Rev Biochem Mol Biol 43, 89-134 (2008)
A Simple Silica-based Method for Metagenomic DNA Extraction from Soil and Sediments
Rojas-Herrera, R., Narvaez-Zapata, J., Zamudio-Maya, M. and Mena-Martinez, M. E.
Mol Biotechnol 40, 13-7 (2008)
Isolation of a low-temperature adapted lipolytic enzyme from uncultivated micro-organism
Roh, C. and Villatte, F.
J Appl Microbiol 105, 116-23 (2008)
Novel precursor-derived Si-C-N ceramic material for purification application
Roh, C., Lee, S. H. and Francois, V.
J Chromatogr A 1179, 145-51 (2008)
A metagenomic analysis of soil bacteria extends the diversity of quorum-quenching lactonases
Riaz, K., Elmerich, C., Moreira, D., Raffoux, A., Dessaux, Y. et al.
Environ Microbiol 10, 560-70 (2008)
Crystal structure and putative function of small Toprim domain-containing protein from Bacillus stearothermophilus
Rezacova, P., Borek, D., Moy, S. F., Joachimiak, A. and Otwinowski, Z.
Proteins 70, 311-9 (2008)
Phototroph genomics ten years on
Raymond, J. and Swingley, W. D.
Photosynth Res 97, 5-19 (2008)
Crystal structure of a conserved protein of unknown function (MJ1651) from Methanococcus jannaschii
Rao, K. N., Burley, S. K. and Swaminathan, S.
Proteins 70, 572-7 (2008)
Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton
Quaiser, A., Lopez-Garcia, P., Zivanovic, Y., Henn, M. R., Rodriguez-Valera, F. et al.
Environ Microbiol (2008)
Two-component signal transduction systems of Xanthomonas spp.: a lesson from genomics
Qian, W., Han, Z. J. and He, C.
Mol Plant Microbe Interact 21, 151-61 (2008)
Biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a Zn ribbon-like domain
Proudfoot, M., Sanders, S. A., Singer, A., Zhang, R., Brown, G. et al.
J Mol Biol 375, 301-15 (2008)
Synthesis and solid-state study of supramolecular host-guest assemblies: Bis[6-O,6-O'-(1,2:3,4-diisopropylidene-alpha-D-galactopyranosyl)thiophosphoryl] dichalcogenides
Potrzebowski, M. J., Potrzebowski, W. M., Jeziorna, A., Ciesielski, W., Gajda, J. et al.
J Org Chem 73, 4388-97 (2008)
Metagenomic analysis of a freshwater toxic cyanobacteria bloom
Pope, P. B. and Patel, B. K.
FEMS Microbiol Ecol 64, 9-27 (2008)
Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre
Pham, V. D., Konstantinidis, K. T., Palden, T. and Delong, E. F.
Environ Microbiol (2008)
Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal
Peterson, S. B., Warnecke, F., Madejska, J., McMahon, K. D. and Hugenholtz, P.
Environ Microbiol (2008)
Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases
Peterson, D. A., Frank, D. N., Pace, N. R. and Gordon, J. I.
Cell Host Microbe 3, 417-27 (2008)
"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division
Pelletier, E., Kreimeyer, A., Bocs, S., Rouy, Z., Gyapay, G. et al.
J Bacteriol 190, 2572-9 (2008)
Fungi and inflammatory bowel diseases: Alterations of composition and diversity
Ott, S. J., Kuhbacher, T., Musfeldt, M., Rosenstiel, P., Hellmig, S. et al.
Scand J Gastroenterol 43, 831-41 (2008)
A nanostructure-initiator mass spectrometry-based enzyme activity assay
Northen, T. R., Lee, J. C., Hoang, L., Raymond, J., Hwang, D. R. et al.
Proc Natl Acad Sci U S A 105, 3678-83 (2008)
Crystal structure of aminopeptidase N from human pathogen Neisseria meningitidis
Nocek, B., Mulligan, R., Bargassa, M., Collart, F. and Joachimiak, A.
Proteins 70, 273-9 (2008)
Exploiting the mosaic structure of trans-acyltransferase polyketide synthases for natural product discovery and pathway dissection
Nguyen, T., Ishida, K., Jenke-Kodama, H., Dittmann, E., Gurgui, C. et al.
Nat Biotechnol 26, 225-33 (2008)
Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics
Neufeld, J. D., Chen, Y., Dumont, M. G. and Murrell, J. C.
Environ Microbiol 10, 1526-35 (2008)
Population proteomics: investigation of protein diversity in human populations
Nedelkov, D.
Proteomics 8, 779-86 (2008)
Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance
Nakagawa, S. and Takai, K.
FEMS Microbiol Ecol 65, 1-14 (2008)
[Structural and functional proteomics consortium for research on the proteins working in brain and nervous system]
Nakagawa, A.
Tanpakushitsu Kakusan Koso 53, 616-9 (2008)
Comparative modeling in structural genomics
Moult, J.
Structure 16, 14-6 (2008)
A metagenomic approach to the identification of UDP-glucose 4-epimerase as a menadione resistance protein
Mori, T., Suenaga, H. and Miyazaki, K.
Biosci Biotechnol Biochem 72, 1611-4 (2008)
Marine mimivirus relatives are probably large algal viruses
Monier, A., Larsen, J. B., Sandaa, R. A., Bratbak, G., Claverie, J. M. et al.
Virol J 5, 12 (2008)
Taxonomic distribution of large DNA viruses in the sea
Monier, A., Claverie, J. M. and Ogata, H.
Genome Biol 9, R106 (2008)
Using inferred residue contacts to distinguish between correct and incorrect protein models
Miller, C. S. and Eisenberg, D.
Bioinformatics 24, 1575-82 (2008)
Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634
McCleverty, C. J., Columbus, L., Kreusch, A. and Lesley, S. A.
Protein Sci 17, 869-77 (2008)
Identification and characterization of novel poly(DL: -lactic acid) depolymerases from metagenome
Mayumi, D., Akutsu-Shigeno, Y., Uchiyama, H., Nomura, N. and Nakajima-Kambe, T.
Appl Microbiol Biotechnol 79, 743-50 (2008)
Alcoholism: protein expression profiles in a human hippocampal model
Matsumoto, H. and Matsumoto, I.
Expert Rev Proteomics 5, 321-31 (2008)
Crystal structure of 2-keto-3-deoxygluconate kinase (TM0067) from Thermotoga maritima at 2.05 A resolution
Mathews,, II, McMullan, D., Miller, M. D., Canaves, J. M., Elsliger, M. A. et al.
Proteins 70, 603-8 (2008)
Metagenomic retrieval of a ribosomal DNA repeat array from an uncultured marine alveolate
Massana, R., Karniol, B., Pommier, T., Bodaker, I. and Beja, O.
Environ Microbiol 10, 1335-43 (2008)
Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions
Martin-Cuadrado, A. B., Rodriguez-Valera, F., Moreira, D., Alba, J. C., Ivars-Martinez, E. et al.
ISME J 2, 865-86 (2008)
Doing more than just the structure-structural genomics in kinase drug discovery
Marsden, B. D. and Knapp, S.
Curr Opin Chem Biol 12, 40-5 (2008)
Viral communities associated with healthy and bleaching corals
Marhaver, K. L., Edwards, R. A. and Rohwer, F.
Environ Microbiol (2008)
Next-Generation DNA Sequencing Methods
Mardis, E. R.
Annu Rev Genomics Hum Genet (2008)
Metagenomics and the niche concept
Marco, D.
Theory Biosci 127, 241-7 (2008)
Peptides in DNA delivery: current insights and future directions
Mann, A., Thakur, G., Shukla, V. and Ganguli, M.
Drug Discov Today 13, 152-60 (2008)
Automated technologies and novel techniques to accelerate protein crystallography for structural genomics
Manjasetty, B. A., Turnbull, A. P., Panjikar, S., Bussow, K. and Chance, M. R.
Proteomics 8, 612-25 (2008)
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
Manichanh, C., Chapple, C. E., Frangeul, L., Gloux, K., Guigo, R. et al.
Nucleic Acids Res (2008)
AQP1 expression analysis in human diseases: implications for proteomic characterization
Magni, F., Chinello, C., Raimondo, F., Mocarelli, P., Kienle, M. G. et al.
Expert Rev Proteomics 5, 29-43 (2008)
LC-MS-based metabonomics analysis
Lu, X., Zhao, X., Bai, C., Zhao, C., Lu, G. et al.
J Chromatogr B Analyt Technol Biomed Life Sci 866, 64-76 (2008)
The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata
Liolios, K., Mavromatis, K., Tavernarakis, N. and Kyrpides, N. C.
Nucleic Acids Res 36, D475-9 (2008)
Recovery, purification, and cloning of high-molecular-weight DNA from soil microorganisms
Liles, M. R., Williamson, L. L., Rodbumrer, J., Torsvik, V., Goodman, R. M. et al.
Appl Environ Microbiol 74, 3302-5 (2008)
Evolution of mammals and their gut microbes
Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R. et al.
Science 320, 1647-51 (2008)
Identification of a novel 4-hydroxyphenylpyruvate dioxygenase from the soil metagenome
Lee, C. M., Yeo, Y. S., Lee, J. H., Kim, S. J., Kim, J. B. et al.
Biochem Biophys Res Commun 370, 322-6 (2008)
Enzymic approach to eurythermalism of Alvinella pompejana and its episymbionts
Lee, C. K., Cary, S. C., Murray, A. E. and Daniel, R. M.
Appl Environ Microbiol 74, 774-82 (2008)
Understanding the molecular machinery of genetics through 3D structures
Laskowski, R. A. and Thornton, J. M.
Nat Rev Genet 9, 141-51 (2008)
[Structural proteomics of metabolism-related proteins]
Kuramitsu, S. and Masui, R.
Tanpakushitsu Kakusan Koso 53, 604-7 (2008)
Phylogenetic classification of short environmental DNA fragments
Krause, L., Diaz, N. N., Goesmann, A., Kelley, S., Nattkemper, T. W. et al.
Nucleic Acids Res 36, 2230-9 (2008)
Crystal structures of MW1337R and lin2004: representatives of a novel protein family that adopt a four-helical bundle fold
Kozbial, P., Xu, Q., Chiu, H. J., McMullan, D., Krishna, S. S. et al.
Proteins 71, 1589-96 (2008)
Biomarkers of primary and evolving damage in traumatic and ischemic brain injury: diagnosis, prognosis, probing mechanisms, and therapeutic decision making
Kochanek, P. M., Berger, R. P., Bayir, H., Wagner, A. K., Jenkins, L. W. et al.
Curr Opin Crit Care 14, 135-41 (2008)
Combining the polymerase incomplete primer extension method for cloning and mutagenesis with microscreening to accelerate structural genomics efforts
Klock, H. E., Koesema, E. J., Knuth, M. W. and Lesley, S. A.
Proteins 71, 982-94 (2008)
Characterization of a gene encoding cellulase from uncultured soil bacteria
Kim, S. J., Lee, C. M., Han, B. R., Kim, M. Y., Yeo, Y. S. et al.
FEMS Microbiol Lett 282, 44-51 (2008)
Estimating P-coverage of biosynthetic pathways in DNA libraries and screening by genetic selection: biotin biosynthesis in the marine microorganism chromohalobacter
Kim, E. J., Angell, S., Janes, J. and Watanabe, C. M.
Mol Biosyst 4, 606-13 (2008)
Rapid screening of quorum-sensing signal N-acyl homoserine lactones by an in vitro cell-free assay
Kawaguchi, T., Chen, Y. P., Norman, R. S. and Decho, A. W.
Appl Environ Microbiol 74, 3667-71 (2008)
Biology-inspired synthesis of compound libraries
Kaiser, M., Wetzel, S., Kumar, K. and Waldmann, H.
Cell Mol Life Sci 65, 1186-201 (2008)
Cellulosome gene cluster analysis for gauging the diversity of the ruminal cellulolytic bacterium Ruminococcus flavefaciens
Jindou, S., Brulc, J. M., Levy-Assaraf, M., Rincon, M. T., Flint, H. J. et al.
FEMS Microbiol Lett (2008)
Biochemical and structural characterization of apolipoprotein A-I binding protein, a novel phosphoprotein with a potential role in sperm capacitation
Jha, K. N., Shumilin, I. A., Digilio, L. C., Chertihin, O., Zheng, H. et al.
Endocrinology 149, 2108-20 (2008)
An assessment of actinobacterial diversity in the marine environment
Jensen, P. R. and Lauro, F. M.
Antonie Van Leeuwenhoek 94, 51-62 (2008)
The impact of extremophiles on structural genomics (and vice versa)
Jenney, F. E., Jr. and Adams, M. W.
Extremophiles 12, 39-50 (2008)
PP2A holoenzyme assembly: in cauda venenum (the sting is in the tail)
Janssens, V., Longin, S. and Goris, J.
Trends Biochem Sci 33, 113-21 (2008)
Hidden pathogens uncovered: metagenomic analysis of urinary tract infections
Imirzalioglu, C., Hain, T., Chakraborty, T. and Domann, E.
Andrologia 40, 66-71 (2008)
Characterization of a Deep-Sea Sediment Metagenomic Clone that Produces Water-Soluble Melanin in Escherichia coli
Huang, Y., Lai, X., He, X., Cao, L., Zeng, Z. et al.
Mar Biotechnol (NY) (2008)
Characterizing the regulation of the Pu promoter in Acinetobacter baylyi ADP1
Huang, W. E., Singer, A. C., Spiers, A. J., Preston, G. M. and Whiteley, A. S.
Environ Microbiol 10, 1668-80 (2008)
Ligand supplementation as a method to increase soluble heterologous protein production
Hozjan, V., Guo, K., Wu, X. and Oppermann, U.
Expert Rev Proteomics 5, 137-43 (2008)
Abundant and diverse bacteria involved in DMSP degradation in marine surface waters
Howard, E. C., Sun, S., Biers, E. J. and Moran, M. A.
Environ Microbiol (2008)
Proteases for processing proneuropeptides into peptide neurotransmitters and hormones
Hook, V., Funkelstein, L., Lu, D., Bark, S., Wegrzyn, J. et al.
Annu Rev Pharmacol Toxicol 48, 393-423 (2008)
Evolutionary ecology and multidisciplinary approaches to prospecting for monooxygenases as biocatalysts
Holmes, A. J. and Coleman, N. V.
Antonie Van Leeuwenhoek 94, 75-84 (2008)
Gene prediction in metagenomic fragments: a large scale machine learning approach
Hoff, K. J., Tech, M., Lingner, T., Daniel, R., Morgenstern, B. et al.
BMC Bioinformatics 9, 217 (2008)
Habitat-Lite: a GSC case study based on free text terms for environmental metadata
Hirschman, L., Clark, C., Cohen, K. B., Mardis, S., Luciano, J. et al.
OMICS 12, 129-36 (2008)
Predicting biological networks from genomic data
Harrington, E. D., Jensen, L. J. and Bork, P.
FEBS Lett 582, 1251-8 (2008)
The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology
Hallin, P. F., Binnewies, T. T. and Ussery, D. W.
Mol Biosyst 4, 363-71 (2008)
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Crystal structure of the global regulatory protein CsrA from Pseudomonas putida at 2.05 A resolution reveals a new fold
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New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library
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Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution
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The crystal structure of the reduced, Zn2+-bound form of the B. subtilis Hsp33 chaperone and its implications for the activation mechanism
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Harvesting the high-hanging fruit: the structure of the YdeN gene product from Bacillus subtilis at 1.8 angstroms resolution
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Acta Crystallogr D Biol Crystallogr 60, 1101-7 (2004)
Optimum solubility (OS) screening: an efficient method to optimize buffer conditions for homogeneity and crystallization of proteins
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Acta Crystallogr D Biol Crystallogr 60, 1670-3 (2004)
On the equivalence between a commonly used correlation coefficient and a least-squares function
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Lectin-based structural glycomics: glycoproteomics and glycan profiling
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The NMR solution structure of the 30S ribosomal protein S27e encoded in gene RS27_ARCFU of Archaeoglobus fulgidis reveals a novel protein fold
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Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 A resolution
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Synchrotron techniques for metalloproteins and human disease in post genome era
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"Reverse-staining" of biomolecules in electrophoresis gels: analytical and micropreparative applications
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Anal Biochem 328, 1-13 (2004)
Metagenomics: application of genomics to uncultured microorganisms
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Microbiol Mol Biol Rev 68, 669-85 (2004)
Bacterial lipases: an overview of production, purification and biochemical properties
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NERD: a DNA processing-related domain present in the anthrax virulence plasmid, pXO1
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A flexible activin explains the membrane-dependent cooperative assembly of TGF-beta family receptors
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Progress towards mapping the universe of protein folds
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Gram-positive DsbE proteins function differently from Gram-negative DsbE homologs. A structure to function analysis of DsbE from Mycobacterium tuberculosis
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Structure of serine acetyltransferase from Haemophilus influenzae Rd
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Sensor domain of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknD, forms a highly symmetric beta propeller
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Structure of Escherichia coli YfdW, a type III CoA transferase
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Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones
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Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model
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The interplay of fold recognition and experimental structure determination in structural genomics
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A novel NAD-binding protein revealed by the crystal structure of 2,3-diketo-L-gulonate reductase (YiaK)
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Structural genomics for Caenorhabditis elegans: high throughput protein expression analysis
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Structure and mechanism of mRNA cap (guanine-N7) methyltransferase
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J Proteome Res 3, 253-60 (2004)
Flow cytogenetics and plant genome mapping
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Crystal structure of the actin binding domain of the cyclase-associated protein
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The structure and ligand binding properties of the B. subtilis YkoF gene product, a member of a novel family of thiamin/HMP-binding proteins
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Structural bases for CRMP function in plexin-dependent semaphorin3A signaling
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Structure determination of fibrillarin from the hyperthermophilic archaeon Pyrococcus furiosus
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Preparation and X-ray crystallographic analysis of the Ca2+-discharged photoprotein obelin
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Crystal structure of a Ca2+-discharged photoprotein: implications for mechanisms of the calcium trigger and bioluminescence
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J Biol Chem 279, 33647-52 (2004)
Crystallization and preliminary X-ray analysis of GlcNAc alpha 1,4Gal-releasing endo-beta-galactosidase from Clostridium perfringens
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A method using active-site sequence conservation to find functional shifts in protein families: application to the enzymes of central metabolism, leading to the identification of an anomalous isocitrate dehydrogenase in pathogens
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Proteins 55, 455-63 (2004)
Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site
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Crystallization and preliminary crystallographic analysis of the Escherichia coli water channel AqpZ
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Genome Res 14, 1188-90 (2004)
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Solution structure of a homodimeric hypothetical protein, At5g22580, a structural genomics target from Arabidopsis thaliana
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Songbird genomics: methods, mechanisms, opportunities, and pitfalls
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Ann N Y Acad Sci 1016, 45-60 (2004)
Biophysical characterization of the complex between double-stranded RNA and the N-terminal domain of the NS1 protein from influenza A virus: evidence for a novel RNA-binding mode
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Biochemistry 43, 1950-62 (2004)
Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii
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Crystal structure of methenyltetrahydrofolate synthetase from Mycoplasma pneumoniae (GI: 13508087) at 2.2 A resolution
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Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): a novel fold with a conserved sequence motif
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The hyperthermophile protein Sso10a is a dimer of winged helix DNA-binding domains linked by an antiparallel coiled coil rod
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Turning protein crystallisation from an art into a science
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Crystal structure of the apo forms of psi 55 tRNA pseudouridine synthase from Mycobacterium tuberculosis: a hinge at the base of the catalytic cleft
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Structural genomics and structural biology: compare and contrast
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Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism
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Assay Drug Dev Technol 2, 313-9 (2004)
Defining the mandate of tuberculosis research in a postgenomic era
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Prevention of aggregation after refolding by balanced stabilization-destabilization: production of the Arabidopsis thaliana protein APG8a (At4g21980) for NMR structure determination
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The importance of redox state in liver damage
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Ann Hepatol 3, 86-92 (2004)
Structural basis for the activity of drugs that inhibit phosphodiesterases
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Protein biophysical properties that correlate with crystallization success in Thermotoga maritima: maximum clustering strategy for structural genomics
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PCR primer selection tool optimized for high-throughput proteomics and structural genomics
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Predicted role for the archease protein family based on structural and sequence analysis of TM1083 and MTH1598, two proteins structurally characterized through structural genomics efforts
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Proteins 56, 19-27 (2004)
Phenotypic profiles and functional genomics in Alzheimer's disease and in dementia with a vascular component
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Genomic characterization of Alzheimer's disease and genotype-related phenotypic analysis of biological markers in dementia
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Pharmacogenomics 5, 1049-105 (2004)
Using an Escherichia coli cell-free extract to screen for soluble expression of recombinant proteins
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J Struct Funct Genomics 5, 69-74 (2004)
Proteomics in the chicken: tools for understanding immune responses to avian diseases
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Poult Sci 83, 552-73 (2004)
Crystal structure of PapA5, a phthiocerol dimycocerosyl transferase from Mycobacterium tuberculosis
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J Biol Chem 279, 30634-42 (2004)
Crystal structure of Bacillus subtilis YdaF protein: a putative ribosomal N-acetyltransferase
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Diversity and population structure of a near-shore marine-sediment viral community
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A practical and robust sequence search strategy for structural genomics target selection
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Bioinformatics 20, 2288-95 (2004)
The status of structural genomics defined through the analysis of current targets and structures
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Pac Symp Biocomput 375-86 (2004)
Crystal structure of gene locus At3g16990 from Arabidopsis thaliana
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Solution structure of the hypothetical protein Mth677 from Methanobacterium thermoautotrophicum: a novel alpha+beta fold
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Crystal structure of the protein from gene At3g17210 of Arabidopsis thaliana
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Molecular mechanisms of GABA(B) receptor activation: new insights from the mechanism of action of CGP7930, a positive allosteric modulator
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High throughput cloning and expression strategies for protein production
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The impact of structural genomics on the protein data bank
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Automated analysis of protein NMR assignments and structures
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Crystal structure of an orphan protein (TM0875) from Thermotoga maritima at 2.00-A resolution reveals a new fold
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Superantigens: structure-function relationships
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G-matrix Fourier transform NMR spectroscopy for complete protein resonance assignment
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Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures
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Mechanistic studies of a flavin-dependent thymidylate synthase
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Biochemistry 43, 10295-301 (2004)
Meeting review: 2003 NIH Protein Structure Initiative Workshop in Protein Production and Crystallization for Structural and Functional Genomics
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Automated protein fold determination using a minimal NMR constraint strategy
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1H, 13C and 15N resonance assignments for methionine sulfoxide reductase B from Bacillus subtilis
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Conserved protein YecM from Escherichia coli shows structural homology to metal-binding isomerases and oxygenases
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Proteins 51, 311-4 (2003)
The 2.2 A resolution structure of RpiB/AlsB from Escherichia coli illustrates a new approach to the ribose-5-phosphate isomerase reaction
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Structure of Escherichia coli ribose-5-phosphate isomerase: a ubiquitous enzyme of the pentose phosphate pathway and the Calvin cycle
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Curr Opin Chem Biol 7, 28-32 (2003)
Deep trefoil knot implicated in RNA binding found in an archaebacterial protein
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Structure of Mycobacterium tuberculosis PknB supports a universal activation mechanism for Ser/Thr protein kinases
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Nat Struct Biol 10, 168-74 (2003)
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Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643
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1H(C) and 1H(N) total NOE correlations in a single 3D NMR experiment. 15N and 13C time-sharing in t1 and t2 dimensions for simultaneous data acquisition
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Crystal structure of Enterococcus faecalis SlyA-like transcriptional factor
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J Biol Chem 278, 20240-4 (2003)
Solution structure of ribosomal protein S28E from Methanobacterium thermoautotrophicum
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The opportunities and challenges of personalized genome-based molecular therapies for cancer: targets, technologies, and molecular chaperones
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Prediction of protein function from protein sequence and structure
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Crystal structure of a flavin-binding protein from Thermotoga maritima
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Crystal structures of a pantothenate synthetase from M. tuberculosis and its complexes with substrates and a reaction intermediate
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Protein Sci 12, 1097-108 (2003)
Carbohydrate microarrays
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Genetic screens and directed evolution for protein solubility
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Violet bioluminescence and fast kinetics from W92F obelin: structure-based proposals for the bioluminescence triggering and the identification of the emitting species
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Biochemistry 42, 6013-24 (2003)
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Prediction of drug metabolism: the case of cytochrome P450 2D6
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Crystal structure of a putative CN hydrolase from yeast
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Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase
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Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli
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Metagenomes of complex microbial consortia derived from different soils as sources for novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli
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Identification and characterization of coenzyme B12-dependent glycerol dehydratase- and diol dehydratase-encoding genes from metagenomic DNA libraries derived from enrichment cultures
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Protein informatics towards function identification
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On the mechanism of chaperone activity of the small heat-shock protein of Methanococcus jannaschii
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Crystal structures of the BtuF periplasmic-binding protein for vitamin B12 suggest a functionally important reduction in protein mobility upon ligand binding
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Crystallization and preliminary X-ray diffraction analysis of lectin-1 from Pseudomonas aeruginosa
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Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals
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Crystal structure of the MazE/MazF complex: molecular bases of antidote-toxin recognition
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Chemical genomics strategy for the discovery of new anticancer agents
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Using structural motif templates to identify proteins with DNA binding function
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Osteopontin: roles in implantation and placentation
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Structures of trinucleotide repeats in human transcripts and their functional implications
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SOMoRe: a multi-dimensional search and optimization approach to molecular replacement
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Ping-pong cross-validation in real space: a method for increasing the phasing power of a partial model without risk of model bias
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Exploiting genomics, genetics and chemistry to combat antibiotic resistance
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Organelle proteomics: implications for subcellular fractionation in proteomics
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Solution NMR structure of ribosome-binding factor A (RbfA), a cold-shock adaptation protein from Escherichia coli
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High-throughput expression, purification, and characterization of recombinant Caenorhabditis elegans proteins
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A global representation of the protein fold space
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A fully integrated protein crystallization platform for small-molecule drug discovery
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The gene cassette metagenome is a basic resource for bacterial genome evolution
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[Blood substitutes--current evidence]
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Recognizing the fold of a protein structure
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Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization
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HEPN: a common domain in bacterial drug resistance and human neurodegenerative proteins
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cctbx news: Fast triplet generator for direct methods, Gallery of direct-space asymmetric units, et. al
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State of the Toolbox: an overview of the Crystallography Toolbox (CCTBX)
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The structure of the carboxyl terminus of striated alpha-tropomyosin in solution reveals an unusual parallel arrangement of interacting alpha-helices
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Biochemistry 42, 614-9 (2003)
Structural genomics of Mycobacterium tuberculosis: a preliminary report of progress at UCLA
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Protein production in Escherichia coli for structural studies by X-ray crystallography
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Structural genomics: computational methods for structure analysis
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Protein Sci 12, 1813-21 (2003)
Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis
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SPINE 2: a system for collaborative structural proteomics within a federated database framework
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Nucleic Acids Res 31, 2833-8 (2003)
Crystal structure of YdcE protein from Bacillus subtilis
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Proteins 53, 320-2 (2003)
Ligand-protein docking: cancer research at the interface between biology and chemistry
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Curr Med Chem 10, 763-7 (2003)
What we have learned about prokaryotes from structural genomics
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Functional assignment based on structural analysis: crystal structure of the yggJ protein (HI0303) of Haemophilus influenzae reveals an RNA methyltransferase with a deep trefoil knot
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Proteins 53, 329-32 (2003)
Modeller: generation and refinement of homology-based protein structure models
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Methods Enzymol 374, 461-91 (2003)
Structural bioinformatics in drug discovery
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Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man
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Crystal structure of thy1, a thymidylate synthase complementing protein from Thermotoga maritima at 2.25 A resolution
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